1o0b: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="1o0b" size="450" color="white" frame="true" align="right" spinBox="true" caption="1o0b, resolution 2.70Å" /> '''CRYSTAL STRUCTURE OF...
 
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1o0b.gif|left|200px]]<br /><applet load="1o0b" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1o0b, resolution 2.70&Aring;" />
'''CRYSTAL STRUCTURE OF L-GLUTAMINE AND AMPCPP BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE'''<br />


==Overview==
==CRYSTAL STRUCTURE OF L-GLUTAMINE AND AMPCPP BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE==
The 2.5 A crystal structure of Escherichia coli glutaminyl-tRNA synthetase, in a quaternary complex with tRNA(Gln), an ATP analog and glutamate, reveals that the non-cognate amino acid adopts a distinct binding mode, within the active site cleft. In contrast to the binding of cognate, glutamine, one oxygen of the charged glutamate carboxylate group makes a, direct ion-pair interaction with the strictly conserved Arg30 residue, located in the first half of the dinucleotide fold domain. The, nucleophilic alpha-carboxylate moiety of glutamate is mispositioned with, respect to both the ATP alpha-phosphate and terminal tRNA ribose groups, suggesting that a component of amino acid discrimination resides at the, catalytic step of the reaction. Further, the other side-chain carboxylate, oxygen of glutamate is found in a position identical to that previously, proposed to be occupied by the NH(2) group of the cognate glutamine, substrate. At this position, the glutamate oxygen accepts hydrogen bonds, from the hydroxyl moiety of Tyr211 and a water molecule. These findings, demonstrate that amino acid specificity by GlnRS cannot arise from, hydrogen bonds donated by the cognate glutamine amide to these same, moieties, as previously suggested. Instead, Arg30 functions as a negative, determinant to drive binding of non-cognate glutamate into a, non-productive orientation. The poorly differentiated cognate amino, acid-binding site in GlnRS may be a consequence of the late emergence of, this enzyme from the eukaryotic lineage of glutamyl-tRNA synthetases.
<StructureSection load='1o0b' size='340' side='right'caption='[[1o0b]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1o0b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O0B FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1o0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o0b OCA], [https://pdbe.org/1o0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o0b RCSB], [https://www.ebi.ac.uk/pdbsum/1o0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o0b ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SYQ_ECOLI SYQ_ECOLI]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o0/1o0b_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1o0b ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1O0B is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with SO4, GLN and AMP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1O0B OCA].
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants., Bullock TL, Uter N, Nissan TA, Perona JJ, J Mol Biol. 2003 Apr 25;328(2):395-408. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12691748 12691748]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Glutamine--tRNA ligase]]
[[Category: Large Structures]]
[[Category: Protein complex]]
[[Category: Bullock TL]]
[[Category: Bullock, T.L.]]
[[Category: Perona JJ]]
[[Category: Perona, J.J.]]
[[Category: AMP]]
[[Category: GLN]]
[[Category: SO4]]
[[Category: amino acid specificity]]
[[Category: engineered trna]]
[[Category: trna-protein complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:42:12 2007''

Latest revision as of 11:00, 14 February 2024

CRYSTAL STRUCTURE OF L-GLUTAMINE AND AMPCPP BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASECRYSTAL STRUCTURE OF L-GLUTAMINE AND AMPCPP BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE

Structural highlights

1o0b is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYQ_ECOLI

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1o0b, resolution 2.70Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1o0b&oldid=4052757"